Search for Variation information by Variation ID:
Detailed information for vg0421282022:
| Variant ID: vg0421282022 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 21282022 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 336. )
Flanking Sequence (100 bp) in Reference Genome:
GGGCACACCTTCCGCTGTCCCGAAAGCTACCCTACATGCTCCGACAGTGACCGCAACGATGTTTAACATCGCAAGTGCCGTCACGGGGATGAACACCGGC[A/G]
ATGAGTCGAAGGTGAACCTCCCAGGGTCAGCACCATCGGTGTTGTCATCGTCATCAGACATGCTTTTGTCCTTGCCGGTGACCTCAAAAACAGTTTCGGA
Reverse complement sequence
TCCGAAACTGTTTTTGAGGTCACCGGCAAGGACAAAAGCATGTCTGATGACGATGACAACACCGATGGTGCTGACCCTGGGAGGTTCACCTTCGACTCAT[T/C]
GCCGGTGTTCATCCCCGTGACGGCACTTGCGATGTTAAACATCGTTGCGGTCACTGTCGGAGCATGTAGGGTAGCTTTCGGGACAGCGGAAGGTGTGCCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.30% | 6.80% | 2.88% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 0.50% | 1.05% | 0.00% | NA |
| All Japonica | 1512 | 73.50% | 19.80% | 6.68% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 97.10% | 0.80% | 2.02% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.40% | 0.43% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 97.30% | 0.80% | 1.91% | 0.00% | NA |
| Temperate Japonica | 767 | 54.00% | 36.40% | 9.65% | 0.00% | NA |
| Tropical Japonica | 504 | 97.80% | 0.00% | 2.18% | 0.00% | NA |
| Japonica Intermediate | 241 | 84.60% | 8.70% | 6.64% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 85.60% | 8.90% | 5.56% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0421282022 | A -> G | LOC_Os04g35020.1 | missense_variant ; p.Leu673Ser; MODERATE | nonsynonymous_codon ; L673S | Average:53.987; most accessible tissue: Callus, score: 95.075 | benign  |
-1.432 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0421282022 | 1.76E-06 | 2.92E-08 | mr1872 | All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0421282022 | NA | 2.26E-09 | mr1709_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0421282022 | NA | 1.19E-07 | mr1880_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |